SMD on Intermembrane Helices

From: Ethan Croitoru (
Date: Tue Dec 22 2020 - 11:15:45 CST

Hi everyone,

I am trying to run an SMD simulation separating two helices in a membrane.
I am doing this for free energy calculations, so I am using colvars to
sample the conformations as they separate. To pull them apart I used a
harmonic on the distance colvar with a forceConstant of 5. However, in my
simulations the helices become disfigured and there is a kink in the
middle. I was wondering if anyone had suggestions as how to pull the
helices apart without them morphing.

Thank you for the help,
Ethan Croitoru

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